def _get_aln_diff(self, blast_result_files):
file_handlers = FileHandlers()
aln_diff = []
for result_file in blast_result_files:
data = self._open_results_file(result_file)
cleaned_data = []
for i in range(len(data)):
fields = data[i].split(' ')
cleaned = file_handlers.clean(fields)
while cleaned.count('') > 0:
cleaned.remove('')
cleaned_data.append(cleaned)
#for line in cleaned_data:
gene_start = ''
pdb_start = ''
while gene_start == '':
for line in cleaned_data:
if ( len(line) == 4 and line[0] == 'Query' ):
gene_start = int(line[1])
break
else:
pass
while pdb_start == '':
for line in cleaned_data:
if ( len(line) == 4 and line[0] == 'Sbjct' ):
pdb_start = int(line[1])
break
else:
pass
seq_name = result_file.split('_')[0] + '_' + result_file.split('_')[3] + '_' + result_file.split('_')[4]
start_site_difference = gene_start - pdb_start
aln_diff.append((seq_name, start_site_difference))
#print aln_diff
return aln_diff
def _open_results_file(self, result_file): file_handlers = FileHandlers() file_paths = file_handlers.search_directory() out_files = file_handlers.find_files(file_paths, 'out') for out_file in out_files: if result_file == file_handlers.get_file_name(out_file): Data = open(out_file, 'r') data = Data.readlines() Data.close() return data
def _pairwise_blast(self, query_files, subject_files, protein=False, nucleotide=False):
file_handlers = FileHandlers()
blast_command = 'blastp' if protein == True else 'blastn'
blast_result_files = []
for query, subject in zip(query_files, subject_files):
blast_result = ( file_handlers.get_file_name(query).split('.')[0] + file_handlers.get_file_name(subject).split('.')[0] + '_blastp.out')
cmd = [blast_command + ' -query ' + query + ' -subject ' + subject + ' > ' + blast_result]
subprocess.call(cmd, shell=True)
blast_result_files.append(blast_result)
return blast_result_files
def _get_fasta_file_paths(self):
query_files = []
subject_files = []
for i in range(len(self.sequence_annotations)):
organism_id = settings.ORGANISM_MAP[self.sequence_annotations[i][2].upper()]
file_handlers = FileHandlers()
file_paths = file_handlers.search_directory()
fasta_files = file_handlers.find_files(file_paths, 'fasta')
for fasta_file in fasta_files:
if ( self.sequence_annotations[i][1] + '_' + organism_id ) == file_handlers.get_file_name(fasta_file).split('.fasta')[0]:
query_files.append(fasta_file)
elif ( self.sequence_annotations[i][1] + '_' + self.filename + '_chain-' + self.sequence_annotations[i][0] ) == file_handlers.get_file_name(fasta_file).split('.')[0]:
subject_files.append(fasta_file)
return query_files, subject_files
def _mkdir(self):
file_handlers = FileHandlers()
file_handlers.make_results_folder(self.dir_path.split('/')[-1])
def _mkdir(self):
file_handlers = FileHandlers()
file_handlers.make_results_folder(self.dir_path.split('/')[-1])
